June 5th 2024

Why do we monitor vegetation?

  • Many plant species respond quickly to land management actions
  • Serve as indicators of whether an area is moving in a more-or-less desirable direction
  • Inform us whether a management action needs to be abandoned, increased, or maintained
  • Serve as the main constituent of habitat quality
  • Note we will not cover demography today.

What variables are typically monitored?

  • Absolute & Relative Cover How much of an area has vegetation? How is this cover composed by species and functional groups?
  • preventing erosion, characterizing habitat.
  • Abundance, Frequency, Density Are individual plants becoming patchier in areas? Is the population declining?
    • Are actions too concentrated to microsites? Is a valuable resource declining?
  • Diversity How many species are there? How are their abundances distributed? Is an area down to only a few species?
    • Overall ecosystem integrity, assessing conservation priorities.

How do we measure plant absolute cover?

  • Depends on vegetation type, and annual climatic variability

  • Forest

    • Line Intercept
  • Grassland & Savannah

    • Line Intercept (LI) & Line-Point Intercept (LPI)
    • (Historic) Daubenmire
  • Small plants!

    • Grids with equal area cells
    • most subjective of the methods
    • complicated by time of sampling

How do we measure plant abundance, frequency, and density?

  • Belt Transects (abundance)
    • plants are very sparse - pop. census size
    • set up around LPI transects
  • Nested Quadrats (frequency)
    • monitor multiple species simultaneously - spatial distribution / stability of populations
    • Daubenmire frames also used
  • Quadrats (density)
    • plants are moderately abundant - pop. census size, spatial distribution

How do we measure diversity?

  • Can be done by wandering around areas…
  • Quadrats
    • Generally much larger than in other types of sampling
    • Fewer replicates
  • Need to be orientated to cross along environmental gradients
  • The gold standard: Modified Whittaker
    • MW has two less intensive follow-up variants, the ‘Intensive’ and ‘Extensive’
    • I&E plots can characterize microhabitats (use determined via rarefaction)
    • takes a long time…

What is Floristic Quality?

‘… tolerance of anthropogenic disturbance and exclusivity to remnant habitats are the only validated criteria for defining FQA.’

‘…FQA conveys two things about high conservative species: (1) All else being equal, they have greater conservation value, and (2) they reflect a site’s history of minimal disturbance and degradation.’

— Spyreas 2019

  • Useful for identifying high-quality remnant habitat
  • Essentially a format for prioritizing land management decisions, especially active management
  • We know we cannot restore everywhere, preventing degradation is key, we can shift certain activities to areas of less conservation values

What do C-values mean?

  • Vary by each administrative unit they are generated for
  • Reflect the purpose of monitoring

’… the coefficient applied to each taxon represents a rank based on observed behavior and patterns of occurrence in Illinois plant communities and our confidence that a taxon is remnant (natural area) dependent.

Species given a C value of 0-1 are taxa adapted to severe disturbances, particularly anthropogenic disturbances…

Species with a C value of 2-3 are associated with somewhat more stable, though degraded, environments.

Species with coefficients 4-6 include many dominant or matrix species for several habitats; they have a high consistency of occurrence within given community types.

Species with C values 7-8 are taxa we associate mostly with natural areas, but that can be found persisting where the habitat has been degraded somewhat.

Species with coefficients 9-10 are considered to be restricted to high-quality natural areas.’

— Taft et al. 1997

Calculations

Mean Coefficient of Conservatism \[ \overline{C} = \frac{\sum{} C_i}{S} \]
  • \(C_i\) in particular \(C\) is the Conservatism Value (C-Value), for each \(_i\) of the \(S\) at the site
    • \(S\) is the number of species included in the calculation
    • \(\overline{C}\) is the Mean Coefficient of Conservatism, or for short Mean C
    • \(\sum{}\) is an operator, meaning that we will sum all C-Values, \(C\)

Floristic Quality Index \[ FQI = \overline{C} * \sqrt{S} \]
  • \(\overline{C}\) is the Mean Coefficient of Conservatism, or for short Mean C
    • \(\sqrt{S}\) is the square root of the number of species included in the calculation

What do we mean by Species Richness?

  • The number of plant taxa in an area; also referred to as \(\gamma-\text{diversity}\)
  • Measuring it can be difficult (time intensive), as many plants are locally rare
  • Progress towards characterizing it can be achieved via rarefaction
  • \(\gamma-\text{diversity}\) , and it’s measurement, is influenced by two main traits
    • the number of species per sub-habitats (\(\alpha-\text{diversity}\))
    • the turnover in species between sub-habitats (\(\beta-\text{diversity}\))

Reading Plots

  • Boundary Decisions
    • Are plants rooted in the plot?
    • Which side of the plots are plant rooted in?
  • Order to reading?
    • Nested quadrats go from smallest to largest plot
      • Only record new species along the way
      • If same species is present in ‘2’ as in ‘1’ do not record.
  • Avoiding double counting
    • search methodically following a single direction
    • Avoid trampling
  • Search in 1/2m wide swaths
Colored areas are "In" a plot.

Colored areas are “In” a plot.

Management Decisions - Species Cover

  • Cover of species naturally ebb and flow
  • Certain management actions can increase cover of some species, while vastly decreasing cover of others
  • Many of the decreasing species may be important for wildlife, or ecosystem function (e.g. water retention, soil stability)
Rotating cattle near Wisdom MT. *Agricultural Funders News*

Rotating cattle near Wisdom MT. Agricultural Funders News

Management Decisions - Vegetation Similarity

  • If we want to restore an area, what is our target?
    • Example: We may want X% absolute cover of broad leaved shrubs w/ < X% relative cover of species Y
    • But where do we get these standards from?
  • Reference site, an area with similar soils & climate to our site
    • altered site should be able to produce a veg community similar to the reference
  • Can we expect areas with similar vegetation to respond similarly to management actions?
    • e.g. fire, grazing cattle/sheep/goats, removal of invasives?
Lanphere Dunes Preserve CA. Reference Site for Coastal backdunes in early seral state

Lanphere Dunes Preserve CA. Reference Site for Coastal backdunes in early seral state

Management Decisions - Species Richness

  • Ecosystem resilience often found to relate to the number of species in an area
    • Loss of species may allow proliferation of invasive species
  • \(\alpha-\text{diversity}\) let’s us know whether we have a good representation of native species at site
  • \(\beta-\text{diversity}\) let’s us know that the site is not becoming more homogenous, i.e. breaking down
  • \(\gamma-\text{diversity}\) let’s us know species can recruit from local areas back to more disturbed areas

Management Decisions - FQA

  • Should areas with more remnant species be prioritized for active management? and why
    • Some species cannot be ‘added’ back in via restoration
    • These areas maybe managed to reduce further anthropogenic impacts, e.g. invasive removal, disallow certain recreation activities.
    • Some areas with higher C-values likely to still harbor rare-species, impetus to survey.
  • Use Mean C, or FQI to detect these areas.
Spraying Weeds Kenai Fjords AK *National Park Service*

Spraying Weeds Kenai Fjords AK National Park Service

A Usage Example

  • See Benkendorf & Holsinger 2023
  • Ca. 250 plots of opportunistic species richness data, collected over 5 years
  • Ca. 860,000 acre area, use spatial statistics and regression techniques to identify features correlating with high FQI
    • Decision:
      • Do we restore areas at less than 7,000 feet? No, unless burned.

Our activity for the early afternoon

  • Compare two different parts of McDonald Woods, Upland White Oak & Swamp White Oak
  1. Assess how quadrats capture species richness
  2. Do sites differ in their Mean C, FQI, or Wetland Indicator status?
  3. Determine appropriate quadrat sizes for future monitoring
  4. Consider similarity of microhabitats across sites

Methods

  • Record all ‘eudicot’ plant species rooted in nest #1
    • Move to nest #2 and record only the species not found in nest #1
    • Continue to do this for all 4 nests
  • After completing the nests, record all plant species not found in the nests, which are present in the final 1x1m square
  • Each person should be able to read a plot once, each person should record
  • DON’T WORRY ABOUT THE SPECIES IDs

Analyses

  • Carried out in R version 4.4.0 (2024-04-24) on linux-gnu
  • iNEXT (Chao et al. 2014, Hsieh et al. 2024) for rarefaction, used to assess sampling completeness.
  • rstatix (Kassambara 2024) for t.test, used to determine whether differences exist between sites.
  • vegan (Oksanen et al. 2024) for Non-metric multiDimensional Scaling (NMDS), are portions of sites more similar to each other
  • FQA Values, Taft et al. 1997, downloaded from https://universalfqa.org/ which may have FQA values for your area too!

Analysis 1 - Are we capturing a representative amount of the species diversity?

  • Not all species are equally common, and detection of locally rare species is difficult
  • We can assess sampling completion using rarefaction, and random shuffling of plots
  • If the number of species (Y axis), increase greatly via extrapolation, then we should sample more plots



Analysis 2 - Are the two sites notably different?

  • FQI reflects the history of disturbance at a site, the sites disturbance histories vary
  • Hypothesis: the Swamp white Oak section has less historic anthropogenic disturbance
  • Null Hypothesis: the FQI of the two sites do not differ
  • Two-sided Wilcoxon Signed Rank Test, data are unpaired
  • Easy method: compare the central tendency of all quadrats per site





Analysis 3 - What Quadrat size can we use to determine frequency of indicator species?

  • It can be difficult to determine the appropriate plot size for monitoring species
  • Nests allow us to try different options readily
  • For expedited monitoring carried out across large domains, finding an optimal size is important
  • We want a species to show up in 20-80% of plots of various sizes
  • our data are pilot data for future monitoring
Species Nest Frequency
A 2 0.33
B 1 0.42
C 1 0.33
D 4 0.42
E 3 0.33
F 1 0.25
G 1 0.33
H 1 0.33
I 4 0.25
J 4 0.42

Analysis 4 - Are certain microhabits more similar across than between sites?

  • Some plots may have more similarities to plots at the other site
  • This may indicate each site has pockets in similar states